MuTect

• Welcome to the MuTect Support Forum

  Answered Announcement 624 views 1 comment 0 points Most recent by Naji May 14
• MuTect has been published and is now freely available!

  Announcement 667 views 0 comments 1 point Started by kcibul February 13
• Could MuTect be suitably applied on ChIP-seq data?

  Answered 10 views 1 comment 0 points Most recent by kcibul June 17
• If the result of Mutect contains all Germline mutaions

  Answered 37 views 1 comment 0 points Most recent by umar June 11
• Number of KEEP vs. REJECT calls

  Answered ✓ 165 views 6 comments 0 points Most recent by umar June 10
• Downsampling

  19 views 0 comments 0 points Started by umar June 10
• Contamination of samples

  16 views 0 comments 0 points Started by umar June 10
• How could I get Indelocator latest version?

  Answered 38 views 2 comments 0 points Most recent by Yujian June 7
• problem in mutect parallel processing

  Answered 47 views 1 comment 0 points Most recent by gpleo June 7
• Temporary files

  Answered ✓ 63 views 2 comments 0 points Most recent by kmdaily June 4
• vcf output question

  Answered 98 views 3 comments 0 points Most recent by kmsquire June 4
• MuTect Bam Input

  Answered ✓ 74 views 2 comments 0 points Most recent by shingwan June 4
• MuTec without dbSNP

  Answered 241 views 3 comments 0 points Most recent by kcibul June 4
• how does use of COSMIC in MuTect influence # of mutations called in known cancer genes vs. others

  Answered 110 views 1 comment 0 points Most recent by kcibul June 4
• FSLockWithShared - WARNING: Unable to lock file

  Answered 43 views 1 comment 0 points Most recent by kcibul June 4
• Does MuTect work with reduced bam files produced by Reduce Reads?

  Answered 86 views 1 comment 1 point Most recent by kcibul June 4
• strand biais details

  Answered 35 views 1 comment 0 points Most recent by kcibul June 4
• fraction_contamination and unrelated status

  Answered ✓ 74 views 6 comments 0 points Most recent by darbrob June 4
• Call "KEEP" "REJECT" option to fine tune filters for poor_mapping_region_alternate_allele_mapq fail

  Answered 109 views 3 comments 0 points Most recent by kcibul June 4
• Parallelizing Mutect

  Answered 132 views 2 comments 0 points Most recent by kcibul June 4
• COSMIC and dbSNP files for MuTect

  Answered ✓ 1.5K views 37 comments 0 points Most recent by shingwan June 3
• extended output columns

  Answered 220 views 6 comments 0 points Most recent by ltonon May 21
• Recommended Syntax for unmatched tumor

  Answered ✓ 319 views 8 comments 0 points Most recent by kcibul April 30
• java.lang.IllegalArgumentException: Comparison method violates its general contract!

  Question 52 views 1 comment 0 points Most recent by seandavi April 25
• Bug report: java.lang.IllegalArgumentException: Comparison method violates its general contract!

  Answered ✓ 260 views 3 comments 0 points Most recent by kcibul April 23
• my mutect coverage.wig result

  Answered ✓ 94 views 1 comment 0 points Most recent by kcibul April 23
• Base quality score recalibration needed?

  Answered 82 views 1 comment 0 points Most recent by kcibul April 23
• VCF output

  Answered ✓ 461 views 8 comments 1 point Most recent by vyellapa April 23
• Where can I get the v63 Cosmic vcf for Mutect？

  Question 69 views 0 comments 0 points Started by Yujian April 23
• negative number of reads processed?

  Answered ✓ 47 views 1 comment 0 points Most recent by kcibul April 16
• Can muTect use a different tmp location

  Answered 82 views 3 comments 0 points Most recent by kmdaily April 16
• somatic mutation site REJECT only because of "DBSNP Site"

  Question 135 views 1 comment 0 points Most recent by circlez April 13
• Intervals to enter for whole exome sequencing data?

  Answered ✓ 154 views 3 comments 0 points Most recent by kcibul April 8
• MuTect in High Confidence (HC) mode

  Answered 237 views 3 comments 0 points Most recent by kcibul April 5
• BQ in VCF file for MuTect

  Question 50 views 0 comments 0 points Started by pkuerten April 5
• Can MuTect be used for other cancer samples than normal-tumor pairs?

  Question 123 views 0 comments 0 points Started by anne_bruun April 3
• How can I make/or get interval file?

  Answered ✓ 209 views 3 comments 0 points Most recent by bd5fh2 April 2
• dbsnp vcf file error

  Question 93 views 0 comments 0 points Started by moonhj April 1
• can MuTect downsample a BAM file?

  Answered ✓ 98 views 3 comments 0 points Most recent by kcibul April 1
• About running options and parsing output file.

  Answered 185 views 4 comments 0 points Most recent by kcibul April 1
• Running mutect in a queue

  78 views 1 comment 0 points Most recent by kcibul April 1
• Running muTect with SOLiD BAMs

  Answered 101 views 2 comments 0 points Most recent by kcibul March 29
• VQSR and MuTect?

  Question 101 views 0 comments 0 points Started by dwaggott March 21
• Cosmic files and incompatible contigs error

  Answered ✓ 131 views 3 comments 0 points Most recent by kcibul March 12
• mutect latest version and pre-released version

  Question 108 views 1 comment 0 points Most recent by huyvuong March 8
• Tumor and normal in a merged bam file

  169 views 2 comments 0 points Most recent by dklevebring March 7
• No_et and proxy errors

  Answered ✓ 106 views 6 comments 0 points Most recent by jellul March 6
• Panel of Normals

  Question 106 views 0 comments 0 points Started by dwaggott March 5
• Mutect on tumor bams alone

  Answered 164 views 1 comment -1 point Most recent by kcibul March 4
• hg19_cosmic_v54_120711.vcf

  Answered 233 views 1 comment 0 points Most recent by kcibul February 27
• muTect ressources

  216 views 2 comments 0 points Most recent by ltonon February 27
• Can muTect run with single-end read BAMs as well?

  Answered 102 views 1 comment 0 points Most recent by kcibul February 26
• How to download MuTect?

  Answered 231 views 2 comments 0 points Most recent by Yujian February 25
• IllegalArgumentException while executing MuTect

  Answered 156 views 1 comment 0 points Most recent by kcibul February 21
• Can you explain me why the following SNV are rejected ?

  Answered 165 views 1 comment 0 points Most recent by kcibul February 21
• Changing or Removing Filters

  Answered 194 views 1 comment 0 points Most recent by kcibul February 21
• Panel of normals

  Question 191 views 0 comments 0 points Started by fmarass February 20
• Getting read-level stats for MuTect output

  Answered ✓ 227 views 2 comments 0 points Most recent by ksikora February 18
• Comparison method violates its general contract!

  Answered ✓ 811 views 10 comments 0 points Most recent by Geraldine_VdAuwera February 15
• strand bias

  Answered 292 views 1 comment 0 points Most recent by kcibul February 13
• How is the power calculated?

  Answered 207 views 4 comments 0 points Most recent by kcibul February 13
• Filtering out "noisy reads"?

  Answered ✓ 169 views 2 comments 0 points Most recent by jstjohn December 2012
• Obtain a copy?

  Answered 141 views 1 comment 0 points Most recent by kcibul December 2012
• Is MuTect part of the GATK v2+now?

  Answered ✓ 275 views 1 comment 0 points Most recent by Geraldine_VdAuwera November 2012
• MuTect and SomaticIndelDetector

  Answered ✓ 444 views 1 comment 0 points Most recent by kcibul October 2012
• Preferred Java(JRE) version to be used for MuTect

  Answered ✓ 252 views 2 comments 0 points Most recent by vaibhavvsk August 2012